How do I understand -Z option of infernal cmscan?
1 answer
To calculate Z please visit this link and use the function
esl-seqstat my_reference.fasta*
- reference fasta should be your genome.
E-score: The E-value is the statistical significance of the hit: the number of hits we’d expect to score this highly in a database of this size (measured by the total number of nucleotides) if the database contained only nonhomologous random sequences. The lower the E-value, the more significant the hit.
Z: This option ensures that the reported E-values are accurate.
I hope that his helps:
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I believe the question about
-Zhas been answered already.As for the
E-value, it is basically the number of matches you would expect to get purely by chance that are of a similar quality as the current match (or better). So if you have anE-valueof 1, you could expect to get up to one extra match (purely by chance) whose alignment to the query is as good as the match you're looking at currently.